gplots statistics

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gplots specifications


Unique identifier OMICS_22070
Name gplots
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.0.1
Stability Stable
stats, grid, gtools, MASS, KernSmooth, caTools, gdata, R(≥3.0)
Maintained Yes




No version available



  • person_outline Gregory Warnes
  • person_outline Gregory Warnes

gplots citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] l clustering of the samples the rlog normalization in DESeq2 was applied. We used the R library pheatmap for sample clustering (euclidian distance, complete linkage clustering) and heatmap.2 from the gplots package to visualize differentially expressed genes (Pearson correlation and ward.D clustering). […]


Food Starch Structure Impacts Gut Microbiome Composition

PMCID: 5956147
PMID: 29769378
DOI: 10.1128/mSphere.00086-18
call_split See protocol

[…] analysis (PCoA) plots, and microbial network maps. Metagenomic function was predicted using PICRUSt () online Galaxy version by the method of Umu et al. (). Heat maps were generated using Calypso and gplots package in R.The White’s nonparametric t test and Kruskal-Wallis H test were performed to compare the relative abundance of genera for two groups and more than three groups, respectively. Stati […]


“Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets”

BMC Infect Dis
PMCID: 5952419
PMID: 29764370
DOI: 10.1186/s12879-018-3127-4
call_split See protocol

[…] package in R [] was used to normalize the counts and call differential expressions. Principal Component Analysis (PCA) was used for data visualization. Hierarchical clustering was performed with the gplots package in R. The ROC curve was plotted with the pROC package in R. Functional and network analyses of differentially expressed genes were performed using Ingenuity Pathway Analysis (IPA, Ingen […]


Cell of origin and mutation pattern define three clinically distinct classes of sebaceous carcinoma

Nat Commun
PMCID: 5951856
PMID: 29760388
DOI: 10.1038/s41467-018-04008-y

[…] r gene sets: all genes with variance >1.0, and the full transcriptome. Hierarchical clustering was performed on the correlation matrix in R, using the default parameters of the heatmap.2 package from gplots version 3.0.1. […]


Parental haplotype specific single cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Nat Commun
PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] Visualization: The data was visualized using the R packages gplots, ggplot2, and Markdown Reports.Transcriptional analysis: Single cells from female germ cells our dataset and from Guo et al., 2015 (Gene Expression Omnibus (GEO) database GSE63818) with at leas […]


The extent of liver injury determines hepatocyte fate toward senescence or cancer

PMCID: 5951829
PMID: 29760381
DOI: 10.1038/s41419-018-0622-x

[…] Fig. 5We also built up heatmaps for genes annotated different Gene Ontology terms about aging, cell proliferation or cell cycle, or for genes known as hepatocellular carcinoma markers using R package gplots. Similarly, all these heatmaps showed that the gene expression profiles in C 8w + A 4w group were separated with which in C 8w and C 12w, and the profilers in C 8w and C 12w were clustered to e […]


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